Thanks Matt.
This kind of worked. The region I want to project is smaller than the
entire simulation domain on the face of the projection. When I made the
projection, it left the projected region the same size relative to the
entire simulation domain and filled in the parts of the domain not
projected with white space. Is there a way I can trim the white space,
or rather have add_projection size the projection to fit the plotting
space?
I've attached an image to show you what I mean.
Thanks so much!
Christine

Dear yt users,
I have the following problem with my yt installation: when I start
ipython or iyt I get the following message:
WARNING: Readline services not available on this platform.
WARNING: The auto-indent feature requires the readline library
and so many useful features (like tab-completion) don't work.
I have another Python installation on my machine, and there it all
works and does not have this warning.
I can bear with the annoying editing, but now I wanted to use the
sqlite3 library, and it is the same - it works from the other Python
installation, but not from the one within yt.
How do I tell the yt installation where to look for these libraries?
Thanks for your help,
Irina

Hi all,
After a few days of hard work, Britton, Matt, and I are pleased to
announce that a major reorganization of yt is complete. This is the
biggest part of what will become yt-2.0, and encompasses nearly all of
the codebase. We have pushed it to the tip of the yt branch in the
hg repository today. PLEASE NOTE you MUST reclone (not hg pull!) your
mercurial repository from hg.enzotools.org! Just move your old
repository out of the way and do
hg clone http://hg.enzotools.org/yt
Finally, please note that as of today SVN is read only. You can still
use the SVN repository for now, but it will no longer acquire any new
changes.
We have done a good amount of testing, but there are sure to be places
where things break. Please report anything you find to the issue
tracker
(http://yt.enzotools.org/newticket) as soon as you can.
The changes have almost all been organizational, except for the
addition of a new QuadTree method for projections, which Matt pushed
to the yt branch ahead of this. Furthermore, unless you do something
**other** than
from yt.mods import *
*everything* should be exactly the same for all of your scripts. We
would really appreciate it if you could file a ticket
(http://yt.enzotools.org/newticket) if you find anything that imports
only from yt.mods doesn't work.
The biggest change is that the old module Snow Crash-derived module
names (lagos, raven, fido, enki) have been removed, and the code has
been divided up into new set of modules, with descriptive names:
drwxr-xr-x 21 joishi joishi 714 Aug 27 11:49 analysis_modules
drwxr-xr-x 31 joishi joishi 1.0k Aug 28 08:45 data_objects
drwxr-xr-x 15 joishi joishi 510 Aug 26 16:57 frontends
drwxr-xr-x 9 joishi joishi 306 Aug 28 08:45 gui
drwxr-xr-x 46 joishi joishi 1.5k Aug 28 08:45 utilities
drwxr-xr-x 38 joishi joishi 1.3k Aug 28 16:09 visualization
The second biggest change, and perhaps the more important one
(especially to yt developers) is the redesign of how we access
component pieces within and outside of yt. Previously, within yt,
importing modules from one part of the code to another was
accomplished by things like
from lagos import *
in the __init__.py file of another module. This has two negative
effects: first, it pollutes the namespaces with many unnecessary
classes and functions (greatly raising the possibility of a
collision), and second, it creates circular imports which can slow
down import times for yt. In order to solve these two problems, we
emptied out __init__.py of everything except a docstring in every
module and replaced them with api.py files. Each module has a api.py
file containing a list of imports of each class or function wihthin
that module imported individually to the API. For example, here is the
visualization api.py:
from color_maps import \
add_cmap
from plot_collection import \
PlotCollection, \
PlotCollectionInteractive, \
concatenate_pdfs, \
get_multi_plot
from fixed_resolution import \
FixedResolutionBuffer, \
ObliqueFixedResolutionBuffer
from image_writer import \
multi_image_composite, \
write_bitmap, \
write_image, \
map_to_colors, \
splat_points
from plot_modifications import \
PlotCallback, \
callback_registry
In order to use a function from the yt/visualization package, you
would add the following import lines to your script:
from yt.mods import * # this hasn't changed
from yt.visualization.api import PlotCollection
pf = load("AwesomeTown0132")
pc = PlotCollection(pf)
The third major change was to move extensions to analysis_modules.
This will likely affect many people in a purely cosmetic way; for
example, the halo finder is now imported by adding the following line
to your script:
from yt.analysis_modules.halo_finding.api import HaloFinder
a bit wordier, but much cleaner. If you are developing yt, please note
that the api.py file is for EXTERNAL scripts only. Anything INTERNAL
to yt must directly import any class or function necessary by directly
referencing the file it resides in, e.g.: from .fixed_resolution
import FixedResolutionBuffer.
Finally, Volume Rendering has been relocated to the new visualization
module. It should otherwise be unchanged (except the api.py change, of
course).
Full notes on all these changes can be found on the wiki:
http://yt.enzotools.org/wiki/yt-2.0
We hope this will lead to a much cleaner, more hackable, more
understandable yt. yt-2.0 will also include a new, simpler plotting
interface. Please feel free to contact Britton, Matt, or me if you
have any questions or any problems with the new yt.
Thanks!
Jeff
Matt
Britton

Hi All,
according to this recipe:
http://yt.enzotools.org/doc/cookbook/recipes.html#find-clumps
it should be possible to pass a list of clumps to the 'clumps' callback. How do
I do that? How do I turn 'master_clump' into a list of clumps? In particular,
I'd like to pass all the clumps found using that recipe above to the plotting
callback.
Thanks!
_______________________________________________________
sskory(a)physics.ucsd.edu o__ Stephen Skory
http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
________________________________(_)_&#92;(_)_______________

Hi yt users,
I have some basic questions about the units. I'm trying to follow through the
cookbook and help site, but some of it isn't working. Namely, the part about
having it tell me what units some of the fields are in.
When I follow the commands on the page:
http://yt.enzotools.org/doc/howto/objects.html This is what happens:
In: pf=load("EZ2_0000")
In: print(pf.h.field_list)
Out: ['z-velocity', 'Temperature', 'Density', 'particle_velocity_z',
'TotalEnergy', 'Dark_Matter_Density', 'particle_position_z', 'x-velocity',
'particle_position_y', 'y-velocity', 'particle_index', 'particle_position_x',
'particle_mass', 'particle_velocity_x', 'particle_velocity_y']
So, I see DM particle fields, which is what I'm interested in. However, when I
try to find their units, I get:
In: print(pf.field_info["particle_velocity_x"].units)
Out: ---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/adavis/Research/YT/src/yt-1.7-svn/scripts/iyt in <module>()
----> 1
2
3
4
5
AttributeError: 'DerivedField' object has no attribute 'units'
I get the same error for the following fields:
[xyz]-velocity, particle_velocity_[xyz], particle_position_[xyz], Density,
TotalEnergy, Dark_Matter_Density, and particle_index (ok, this shouldn't have
units)
When I try the other method of getting at the units:
pf.field_info["particle_velocity_x"].get_source() , there is nothing there that
says anything about units.
Out: def _Particles(field, data):
io = data.hierarchy.io
if not data.NumberOfParticles > 0:
return na.array([], dtype=dtype)
try:
return io._read_data_set(data, p_field).astype(dtype)
except io._read_exception:
pass
# This is bad. But it's the best idea I have right now.
return data._read_data(p_field.replace("_"," ")).astype(dtype)
And, while field_info["Density"].get_source() works, the same command for
Temperature tells me that the units are g/cm^3, which is obviously wrong.
So, my major question: particle positions seem to be in the [0-1] unit system,
so conversion is simple for them. Particle velocities, however, are unclear.
They look like they're in cm/s, but I'd like to be sure.
thanks!
Andrew
*************************************************************
** Andrew J. Davis andrew.davis(a)yale.edu **
** Dept. of Astronomy 203-432-5119 **
** Yale University www.astro.yale.edu/adavis **
*************************************************************

Greetings,
I've just added a new feature to the EnzoSimulation class that a number of
people have been asking for. If you don't know what EnzoSimulation does,
see here:
http://yt.enzotools.org/doc/extensions/analyzing_an_entire_simulation.html
For people who have been setting Enzo to output every constant number of
cycles, rather than a constant amount of time, the EnzoSimulation class did
not work, as there is no way to know from the parameter file exactly how
many datadumps will get made during the simulation and at what times. Also,
if you do collapse simulations where you are outputting data every time a
new AMR level is reached, it doesn't work for you either. To fix that, I've
added a new keyword, get_data_by_force, that if set to True, will search the
working directory for all directories that match the data dir name
convention. It will then open them all and get times and redshifts by
hand. It takes slightly longer, but only a second or two compared to
previously less than a second.
So to use this, you simply need to do, for example:
import yt.extensions.enzo_simulation as ES
my_run = ES.EnzoSimulation(parameter_file, get_data_by_force=True,
initial_time=0)
And my_run.allOutputs will have your list of datasets.
Britton

Hi,
I have been trying to build yt on Legion cluster at University College London. My default modules are...
Currently Loaded Modulefiles:
1) shared 5) infinipath/base/2.1 9) nedit/5.6
2) intel/fce/10.1.008 6) infinipath/mpi/intel/2.1 10) mrxvt/0.5.4
3) intel/cce/10.1.008 7) torque/2.2.1 11) hdf5/1.6.6
4) intel/mkl/64emt/10.0.2.018 8) moab/5.3.0
I did a module purge. And added gcc module...
Currently Loaded Modulefiles:
1) GCC/4.4.1
But, the install_script.sh crashes when building matplot with the following warning in the yt_install.log...
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/include/python2.6 -c src/path.cpp -o build/temp.linux-x86_64-2.6/src/path.o
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
In file included from /shared/ucl/test/GCC4/lib/gcc/x86_64-unknown-linux-gnu/4.4.1/../../../../include/c++/4.4.1/ext/hash_map:59,
from ./CXX/Extensions.hxx:68,
from src/path.cpp:8:
/shared/ucl/test/GCC4/lib/gcc/x86_64-unknown-linux-gnu/4.4.1/../../../../include/c++/4.4.1/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
Please let me know what could be happening here.
Shankar

I just put Ubuntu 10.04 64bit on my desktop and wanted to get yt going
and ran into an issue with the linux/unix install script. It gets up to
matplotlib and errors out:
Installation will be to
/home/bob/local/yt-unknown
and I'll be logging the installation in
/home/bob/local/yt-unknown/yt_install.log
I think that about wraps it up. If you want to continue, hit enter.
If you'd rather stop, maybe think things over, even grab a sandwich,
hit Ctrl-C.
========================================================================
[hit enter]
Awesome! Here we go.
Downloading HDF5
Downloading hdf5-1.6.9.tar.gz from yt.enzotools.org
Downloading zlib-1.2.3.tar.bz2 from yt.enzotools.org
Downloading Python-2.6.3.tgz from yt.enzotools.org
Downloading numpy-1.4.1.tar.gz from yt.enzotools.org
Downloading matplotlib-0.99.3.tar.gz from yt.enzotools.org
Downloading ipython-0.10.tar.gz from yt.enzotools.org
Downloading h5py-1.2.0.tar.gz from yt.enzotools.org
Setting YT_DIR=/home/bob/local/yt-unknown/src/yt-1.7-svn/
Installing distribute
Installing pip
Installing matplotlib-0.99.3 (arguments: 'matplotlib-0.99.3')
Failure. Check /home/bob/local/yt-unknown/yt_install.log.
bob@keplernix:~/local$
I've attached the yt_install.log to lower the spam content. Thanks in
advance!
-Robert Thompson